A potentially life-changing race is on for asylum seekers who haven't yet lodged their applications for Temporary Protection visas or Safe Haven Enterprise visas.

The federal government has given asylum seekers until October 1 to formally apply for protection, or face deportation.

Approximately 30,500 people in Australia who arrived by boat from August 2012 have been eligible to apply.

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While most have done so, Immigration and Border Protection figures show up to 1,500 people nationally are yet to lodge their applications.

"One of the central reasons is really terrible vulnerability. Extreme vulnerability that many people experience having fled in fear for their lives from their home country, from places like Afghanistan, Iraq, Syria, Rohingya from Myanmar," David Manne, Executive Director of Refugee Legal said.

"One of the key reasons for why some people have not yet applied has been not only that they have been confused, but they have also been very frightened about the process."

Not too late to apply

The pressure is mounting for them to apply before October 1, with the federal government having announced the new deadline in May.

It prompted lawyers and interpreters across Australia to come forward and offer free help for asylum seekers with their visa applications.

David Manne from Refugee Legal was one of those.

He said the application document is complicated and onerous and it's critical people get the free legal assistance available.

"There are forms with over 100 questions, plus a detailed written statement of someone's fears that have to be lodged all in writing and all in English."

Immigration and Border Protection has said it will be assumed those who do not apply before the deadline no longer intend to seek protection in Australia.

Asylum seekers being held in Australian immigration detention on Manus Island have responded to the release of a phone call transcript in which the PM told the US president he could decide who to take or not take in the refugee swap.

"First, they face the prospect of the government not considering any protection visa application in the future. So that is not allowing people to apply for protection as a refugee in Australia. And also ultimately, they face the risk of being deported without even having their case for protection heard," he said.

But it's not too late to apply, with Mr Manne urging anyone who still needs legal help to come forward.

"It is absolutely essential that if anyone in this group hasn't yet applied, that they seek legal help, free legal assistance to understand their rights and to make that application."

Applications can be lodged online and via post.

However, if the application is lodged by post, enough time has to be allowed for it to be received by the Immigation Department before October 1.